Variant report

Variant	rs6661862
Chromosome Location	chr1:62534854-62534855
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1013293	0.84[CEU][hapmap];1.00[CHB][hapmap]
rs12730782	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17379217	0.92[CEU][hapmap];0.89[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2476187	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs2476189	1.00[CHB][hapmap]
rs2476190	1.00[CHB][hapmap]
rs2476191	1.00[CHB][hapmap]
rs2481665	0.84[TSI][hapmap]
rs2498978	0.83[EUR][1000 genomes]
rs2498980	0.83[CEU][hapmap];0.87[EUR][1000 genomes]
rs55725347	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6668421	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs6668600	0.96[CEU][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6670849	0.92[CEU][hapmap];0.84[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs6674622	0.96[CEU][hapmap];0.87[TSI][hapmap];0.94[EUR][1000 genomes]
rs6674784	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6681153	0.81[CEU][hapmap];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1001667	chr1:62407786-62649838	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6661862	NFIA	cis	cerebellum	SCAN
rs6661862	RAVER2	cis	cerebellum	SCAN
rs6661862	TACSTD2	cis	cerebellum	SCAN
rs6661862	ROR1	cis	cerebellum	SCAN

Chromatin state (count:50 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62459200-62550000	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:62460000-62544600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr1:62484400-62562200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:62495200-62544800	Weak transcription	Liver	Liver
5	chr1:62508200-62628400	Weak transcription	Colonic Mucosa	Colon
6	chr1:62515400-62552400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:62519000-62541600	Weak transcription	HMEC	breast
8	chr1:62519000-62550000	Weak transcription	Primary T cells from cord blood	blood
9	chr1:62519000-62550000	Weak transcription	Pancreas	Pancrea
10	chr1:62519000-62552000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:62521800-62546200	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr1:62530800-62541400	Weak transcription	Fetal Kidney	kidney
13	chr1:62532400-62552400	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr1:62532600-62544600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:62532600-62545000	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:62532600-62548800	Weak transcription	Fetal Intestine Small	intestine
17	chr1:62532600-62550000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr1:62532600-62550600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr1:62532600-62552400	Weak transcription	Esophagus	oesophagus
20	chr1:62532600-62557400	Weak transcription	Spleen	Spleen
21	chr1:62532600-62568200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr1:62532600-62569200	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:62532600-62587600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:62532800-62545000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:62532800-62552800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:62532800-62569000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:62533400-62550000	Weak transcription	Fetal Intestine Large	intestine
28	chr1:62533600-62535200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr1:62533600-62536000	Enhancers	Adipose Nuclei	Adipose
30	chr1:62533600-62536200	Enhancers	Rectal Smooth Muscle	rectum
31	chr1:62533800-62535200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr1:62533800-62535400	Enhancers	Fetal Muscle Leg	muscle
33	chr1:62534000-62535000	Enhancers	Fetal Stomach	stomach
34	chr1:62534000-62535600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:62534000-62536200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr1:62534200-62535000	Enhancers	NHEK	skin
37	chr1:62534200-62535200	Enhancers	Fetal Lung	lung
38	chr1:62534400-62536600	Enhancers	Fetal Heart	heart
39	chr1:62534400-62545200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:62534400-62555000	Weak transcription	Ovary	ovary
41	chr1:62534400-62555400	Weak transcription	Left Ventricle	heart
42	chr1:62534600-62535000	Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr1:62534600-62535000	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr1:62534600-62535200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr1:62534600-62535200	Weak transcription	Right Atrium	heart
46	chr1:62534600-62537000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:62534600-62541800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr1:62534800-62535000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:62534800-62535200	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr1:62534800-62535200	Flanking Active TSS	Stomach Smooth Muscle	stomach

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